Here's the Catch

By Sarah Thompson

Lars Rudstam, director of the Cornell Biological Field Station at Shackelton Point and professor of natural resources, holds the shell of a native clam no longer found in Oneida Lake as a result of invasive zebra mussels. Photo: Robert Way

Look over the side of a boat on Oneida Lake in early summer: In some places you can see straight down nearly 18 feet below. The water is clearer than it was two decades ago, when the lake was more often covered with algal blooms, and murky waters sheltered young walleye and yellow perch. When the change in clarity came, it was accompanied by warming waters and invasive species. Scientists at the Cornell Biological Field Station (CBFS) at Shackelton Point have been monitoring changes in Oneida Lake, located northeast of Syracuse, for more than six decades. Researchers there track food chains, nutrient levels, predator-prey interactions, invasive species, and climate, and they are one of many teams in CALS tracking wild fish populations in ecosystems from inland lakes to coastal waters—information crucial to defining sustainability in fisheries for the future.

Oneida Lake is a good model for studying freshwater ecosystems because of its size and depth: At 78.9 square miles, by surface area it’s the largest lake wholly within New York state, with an average depth of 22 feet. Because the lake’s shallow waters mix completely each year, small changes ripple quickly throughout its ecosystem. During the 20th century, more than 75 species of fish were recorded in the lake, from minnows to giant lake sturgeon. Since the 1940s, walleye, bass and perch have dominated the lake’s fisheries; today it’s one of the premier sport fisheries for walleye in the Northeast.

Lars Rudstam, CBFS director and professor of natural resources, described his team’s work as a balancing act. They monitor fish populations and environmental changes for conservation as well as to support recreational fisheries—which on Oneida Lake alone bring in an estimated $20 million a year.

“It’s recreational to anglers but not to the local people who rely on the income for their livelihood,” Rudstam said.

Rudstam and his colleagues have been tracking a series of changes in freshwater lakes, including the Great Lakes. The mid-1970s were marked by a major reduction in phosphorous pollution, thanks to a state ban of phosphates in household detergents and better waste water treatment. Cleaning up the lakes reduced harmful algal blooms, but then populations of zooplankton—tiny animals at the bottom of lake food chains—dwindled. Fewer zooplankton meant less food for prey fish, and the result was disastrous for at least one major Great Lake fishery.

“In Lake Huron, a major decline in the zooplankton population caused a collapse in Chinook salmon. We have cleaner lakes because we’re doing a better job controlling the nutrients going into them, but we need to understand the consequences of these decisions,” Rudstam said.

In 1991, those consequences were compounded by the arrival of the invasive zebra mussel, a bivalve that can filter 1 quart of water per day—straining out large amounts of phytoplankton, or tiny aquatic plants. The zebra mussel’s arrival drastically increased water clarity and quality in Oneida Lake. Today, sunlight penetrates deeper lake waters, allowing growth of underwater weed beds (the preferred habitat for smallmouth bass and sunfish), while making young fish more vulnerable to predators and potentially affecting light-sensitive walleyes.

These complex food chain interactions are difficult to predict and prepare for, which is why CBFS research associate James Watkins ’89, Ph.D. ’11, is trying to gather better information on the feeding habits of important fisheries. In a new project launching this summer, Watkins will monitor Chinook salmon in Lake Ontario by tagging them with sophisticated satellite archival tags, called PSATS, which automatically drop off and transmit their data to satellites. The project will net data on temperature, depth and light in the salmon’s daily habitats, and by extension, those of its prey.

“By finding connections between the lake’s lower food web and fish populations, we’ll learn how to keep the Chinook salmon population healthy so it doesn’t have a similar fate [as those on Lake Huron],” Watkins said.

Planning for changing climate scenarios plays to the strengths of the CBFS, which can tap into six decades of data. Rudstam, together with senior research associate Randy Jackson and their CBFS colleagues, are mining historical records to tease out the effects of climate change on Oneida Lake, whose water temperatures rose by almost three degrees Fahrenheit from 1975 to 2001. By the end of the century, models predict that it will rise by six degrees—reshaping fish populations in favor of warm-water bass over walleye, and potentially bringing back the algae blooms that once earned Oneida Lake the nickname “le lac vert”—the green lake.

Drones on Deck

“With a fleet of Wave Gliders, it takes one week to survey the same area that would take a ship two months. And over those two months, we can get eight snapshots of fish distributions that are less blurry. With better data, we can reach for the holy grail of maximizing harvests from a fishery that is managed sustainably.”
-Charles Greene, professor of earth and atmospheric sciences
Photo: Liquid Robotics, Inc.

Like their CBFS counterparts, Cornell seafaring scientists also are working to strike a more sustainable balance for commercial marine fisheries facing rising demand. According to the Food and Agriculture Organization (FAO) of the United Nations, global production of capture fisheries reached 92.6 million tons in 2013.

“As the world population is growing, it’s going to put more demand on getting food from the sea. We need to protect fish populations from overfishing, but there is no reason why wild fisheries can’t be harvested sustainably,” said Charles Greene, professor of earth and atmospheric sciences.

For Greene, protecting marine fish stocks while sustaining fisheries is a function of better data. Since the 1970s, fisheries agencies have used ship-based acoustic surveys to monitor fish stocks, make predictions, and set fishing season and catch limits. Acoustic surveys are conducted by ships cruising back and forth, transmitting sound at different frequencies into the ocean. When these sound waves hit something—like a school of fish—they scatter back to a transducer, which converts them into visual patterns scientists interpret to estimate the type, size and number of animals in the area.

But acoustic surveys using manned vessels are too expensive and time consuming to do frequently, which constrains their usefulness and quality. To survey the entire west coast of the United States, it takes special low-noise ships two months at a cost of $25,000 per day—and still only gives scientists a rough idea of what’s happening in the ocean at any given time.

“It’s like leaving a camera shutter open for two minutes versus seconds. You get a really blurry picture of where these fish are,” Greene said.

Since 2011, Greene has been collaborating with two companies—Liquid Robotics, Inc. (LRI) and BioSonics—to enable LRI’s autonomous Wave Glider robot to collect the same acoustic data as ships but at substantially lower maintenance and labor costs. The robot consists of a surface float housing electronics and solar panels, tethered by cable to an underwater glider with wings that generate propulsion and a rudder for steering. The glider tows an echo sounder, which transmits and receives the sound signals. It’s ideal for long deployments at sea, with a lightweight body, wireless data transmission and control, and efficient use of wave motion and solar energy for power. This spring, Greene is testing the latest version of the technologies his team developed, and he will be working with U.S. National Marine Fisheries Service scientists to evaluate the prospects of using Wave Gliders to create mobile ocean observing networks.

“With a fleet of Wave Gliders, it takes one week to survey the same area that would take a ship two months. And over those two months, we can get eight snapshots of fish distributions that are less blurry. With better data, we can reach for the holy grail of maximizing harvests from a fishery that is managed sustainably,” Greene said.

The picture of fisheries captured by Nina Overgaard Therkildsen, assistant professor and the newest faculty member in the Department of Natural Resources, is one composed of DNA. It has convinced her that genomics will not only allow fisheries managers to better predict how wild populations will respond to fishing pressure and changing environmental conditions, but it will also give them the tools to identify and protect valuable local genetic variation within species.

“Maintaining fish populations that are adapted to different types of conditions is like maintaining a diversified financial portfolio. The more diversity you have, the greater the chance that something will do well in the future, depending on the changes,” she said.

Therkildsen said scientists are finding that fish are genetically adapted to particular local conditions. To find out what factors drive these adaptations, and how they may enhance survival, Therkildsen is a genetic forensic detective, analyzing the genes of cod collected from Greenland and North Atlantic fisheries, as well as DNA from historical samples of cod otoliths, or ear bones. Using these data, Therkildsen reconstructed what cod looked like genetically 80 years ago to build a picture of Greenland’s booming cod fishery in the 1940s and 1950s before its collapse a decade later. She found that the fishery actually comprised four genetically distinct cod populations: local Greenland cod plus cod from Iceland.

Therkildsen also found that Greenland’s inshore cod—which remained plentiful after the collapse of its large offshore fishery—were a different population from and didn’t breed with offshore cod. Based on this and other data, fisheries managers began separate population assessments and recently reopened Greenland’s inshore cod fishery. It’s an example of biology’s role in sustainable management, and now Therkildsen is flipping the question to identify how commercial fishing changes fish genetics.

“In fisheries, we basically do the opposite of what we do in breeding programs for domestic animals. We fish out the most attractive individuals and leave the rest to produce the next generation. This means that if certain desirable traits—and the genes behind them—are ‘fished out,’ this will change the genetic makeup of the population over time,” she said.

During the last few decades, data show that growth, as well as age and size at maturity, have declined in many commercial fish stocks, indicating a possible loss of reproductive strength. To better understand the genomic basis of these changes, Therkildsen is now sequencing the entire genome of the Atlantic silverside and conducting controlled studies on the effects of fishing selection. She’ll also analyze DNA from otolith samples to see how the species’ genome has changed since the onset of industrial fishing.

Insights from population genetics also are helping turn the tide for vulnerable species, including the long-suffering eastern oyster.

“You used to be able to get oysters on every street corner in Manhattan, but we squandered our natural heritage with pollution and overharvesting,” said Matthew Hare, associate professor of natural resources.

Now scientists are using oysters to help return the Hudson River estuary to a vibrant and productive ecosystem. The goal is to restore this keystone species, whose filter feeding improves water quality and whose reefs protect shoreline, providing habitat for other species. Restoration has been harder than expected. Hare, a population geneticist, suspects problems stem from the limited genetic diversity maintained in restoration oysters produced by hatcheries to repopulate reefs.

To find out exactly how important genetic variation is for survival of oysters in the Hudson River estuary, Hare is launching a new study, funded by the Atkinson Center for a Sustainable Future, to test the hypothesis that genetically diverse hatchery cohorts will perform better in stressful environments than those with a narrow genetic base. This work builds on Hare’s other recent findings, studies showing striking patterns of genetic differentiation within a single estuary.

“Before this, we thought it was the oyster’s natural flexibility that explained its survival in diverse environments. But our genetic data show that different habitats also exert strong selection pressure, causing nearby populations to diverge in their innate environmental tolerances—to salinity, pollution and other stressors—every generation. This means it can matter which adult oysters we choose to breed for restoration of a particular habitat and underscores the benefits of maintaining genetic diversity,” Hare said.

Farm-Raised Flow

Oysters growing on tires in the East River intertidal shoreline.
Photo: NY/NJ Baykeepers

As long as demand exceeds supply, wild fish and shellfish stocks will always be subject to management. One way to reduce demand on wild populations is by increasing supply using aquaculture, or fish farming. Globally, this is exactly what’s happened over the past decade. In 2013, the FAO reported that world production of farmed food fish reached 70.2 million tons—or 43 percent of total world fish production, up from 30.6 percent in 2003.

As the industry has grown, so have concerns about its environmental impact. The majority of aquaculture farms today use net pens placed in coastal waterways, sparking concerns of nutrient pollution from waste, escapees becoming invasive species, and disease outbreaks spreading to wild populations. This is why Michael Timmons, Ph.D. ’79, professor of biological and environmental engineering, believes that indoor recirculating aquaculture systems, or RAS, are the only truly sustainable solution to the supply problem.

“The advantage of RAS is that fish can be stocked much more densely, up to one pound of fish per gallon of water, thus using only a fraction of the water and space to grow the same amount of fish as pond or netting-based systems,” Timmons said.

Since 1985, Timmons has been refining RAS that continuously filter and recycle water through densely packed fish tanks, making them more energy efficient and productive. For the past 20 years, Timmons has taught a short course for and helped small-scale farmers develop aquaponic systems, which combine aquaculture with hydroponics by growing plants—like lettuce, Asian greens or herbs—on beds of gravel or Styrofoam over fish tanks. Water is recirculated from fish to plants, which take up nutrient waste as fertilizer.

Now Timmons has designed a commercial aquaculture system he said could be a game changer for making indoor systems cost competitive with net pens. In a building covering just two acres, his system could produce 1,000 tons of tilapia annually—using 80 percent less energy than conventional systems to produce the same amount of fish per unit of energy.

“Our system uses less than one kilowatt hour per one kilogram of fish produced,” Timmons said.

The key is having very low elevation differences between tanks, pipes and filters, which significantly lowers the water pressure and energy required to recirculate water. This allows Timmons’ system to move 4,000 gallons per minute, per kilowatt.

“It makes the movement of water almost free. And when you have very high water exchange in the system, you have very high water quality—and very high fish productivity and quality,” Timmons said.

City-Raised Seafood

Philson A.A. Warner, research associate for Cornell University Cooperative Extension New York City, specializes in the science of connections, using cutting-edge technologies to connect city youths to their environment, food and futures. Every year, Warner directs students working in his hydroponics, aquaculture and aquaponics labs at Food and Finance High School, New York City’s only culinary arts high school.

The labs use Warner’s patented aquaculture technology and hydroponics systems and are part of students’ mandatory STEM (Science, Technology, Engineering and Math) classes, independent studies and paid internships. They also produce up to a combined 70,000 pounds of seafood and 6,400 heads of lettuce, herbs and other vegetables each year. This bounty supplies the school’s culinary arts classes, cafeteria, catering program and city restaurants.

It’s a “win-win-win situation,” Warner said, introducing inner city youths to an unfamiliar environment while refining his technologies and the related STEM curricula—the Hydroponics Learning Model and Grow With the Flow.

“A lightbulb turns on as they are exposed to not only the array of possibilities in science, technology, agriculture and horticulture—but also the entrepreneurial and economic opportunities,” he said.

This year, students can learn in a new 2,000-square-foot rooftop aquaponics greenhouse at the high school, the first of its kind. But this expansion, compared to conventional farming, will net more food per square foot and more sales without using a lot more energy.